Intermittently closed and open coastal lakes and lagoons (ICOLLs) are ecologically important and hydrologically sensitive estuarine systems. We explore how extreme drought and ICOLL entrance management intersect to influence the geochemical cycling of iron. Opening the ICOLL entrance just prior to an extreme drought in 2019 led to prolonged extremely low water levels, thereby exposing intertidal/subtidal sulfidic sediments and causing oxidation of sedimentary pyrite. Subsequent reflooding of exposed sediments for ∼4 months led to extremely elevated Fe2+(aq) (>10 mM) in intertidal hyporheic porewaters, consistent with Fe2+(aq) release via pyrite oxidation and via reductive dissolution of newly-formed Fe(III) phases. Re-opening the ICOLL entrance caused a rapid fall in water levels (∼1.5 m over 7 d), driving the development of effluent groundwater gradients in the intertidal zone, thereby transporting Fe2+-rich porewater into surface sediments and surface waters. This was accompanied by co-mobilisation of some trace metals and nutrients. On contact with oxic, circumneutral-pH estuarine water, the abundant Fe2+(aq) oxidised, forming a spatially extensive accumulation of poorly crystalline Fe(III) oxyhydroxide floc (up to 25 % Fe dry weight) in shallow intertidal zone benthic sediments throughout the ICOLL. Modelling estimates ∼4050 × 103 kg of poorly-crystalline Fe was translocated into surficial sediments. The newly formed Fe(III)-oxyhydroxides serve as a metastable sink encouraging enrichment of both phosphate and various trace metal(loid)s in near-surface sediments, which may have consequences for future cycling of nutrients, metals and ICOLL ecological function. The additional Fe also may enhance ICOLL sensitivity to similar future drought events by encouraging pyrite formation in shallow (<5 cm) benthic sediments. This system-wide translocation of Fe from deeper sediments into surficial benthic sediments represents a form of geochemical hysteresis with an uncertain recovery trajectory. This study demonstrates how climate extremes can interact with anthropogenic management to amplify ICOLL hydrological oscillations and influence biogeochemistry in complex ways.